Crystal Structure of Monoclinic Ribonuclease-S at 4 Å Resolution

Abstract

A four-Å electron density map was calculated for the monoclinic crystal of ribonuclease-S (RNase-S) based on two heavy-atom derivatives. Close geometrical similarity was found between the two crystallographically independent RNase-S molecules (called molecules ZA and ZB) in this crystal and that (called molecule Y) in the trigonal crystal. Using the rotational and translational parameters relating these three molecules, it was established that the crystallographic two-fold symmetry between the two molecules ZA in the monoclinic crystal was exactly identical to that between the two molecules ZA in the monoclinic crystal was exactly suggesting the tendency of RNase-S molecules to associate in this way although the interaction is weak. The 4-Å difference Fourier maps calculated for the monoclinic crystal established the following conclusions. (1) 4-Thiouridine-2′(3′)-monophosphate binds to the B₁ and R₁ sites like other pyrimidine nucleoside-2′(3′)-monophosphates as expected from previous spectrophotometric studies, but not to the B₁site even at the concentration of 20 mM. An attempt to visualize the photoproduct generated by irradiation of near-ultraviolet light in this complex failed. (2) p-Aminobenzoylglutamic acid, a fragment of folic acid, seems to bind to RNase-S with its benzene ring close to the B₂ site and the α-carboxylate group close to the P₁ site. The model is compatible with most of the chemical results obtained by Sawada et al. ((1977) Biochim. Biophys. Acta 479, 188–197).